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Magnesium chelatase H subunit (ChlH) E660W variant from Synechocystis sp.PCC6803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 0.8-1.2 M sodium citrate and 2 mM dithiothreitol
Crystal Properties Matthews coefficient Solvent content 3.36 63.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 317.55 α = 90 b = 317.55 β = 90 c = 104.43 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 79.39 99.9 0.059 0.997 10.2 5.8 107741
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 0.676 0.49 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6YSG 2.7 79.387 107741 5365 99.904 0.194 0.1919 0.2346 0.2132 69.301
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.288 0.644 1.288 -4.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_3_deg 16.431 r_dihedral_angle_4_deg 15.804 r_lrange_it 8.262 r_lrange_other 8.261 r_dihedral_angle_1_deg 6.734 r_mcangle_it 5.947 r_mcangle_other 5.947 r_scangle_it 5.703 r_scangle_other 5.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_3_deg 16.431 r_dihedral_angle_4_deg 15.804 r_lrange_it 8.262 r_lrange_other 8.261 r_dihedral_angle_1_deg 6.734 r_mcangle_it 5.947 r_mcangle_other 5.947 r_scangle_it 5.703 r_scangle_other 5.703 r_mcbond_it 3.844 r_mcbond_other 3.839 r_scbond_it 3.583 r_scbond_other 3.583 r_angle_refined_deg 1.294 r_angle_other_deg 1.143 r_nbd_refined 0.193 r_symmetry_nbd_other 0.176 r_nbd_other 0.164 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbd_refined 0.117 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19763 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing